X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=3f8175d204631cfb5e6a3a21c5b7ce3cf858dbc3;hb=fa9da54fb97cb2eacb1af7859024d90166bddb8f;hp=af40504bd980a9f7d656ebbf8bbae574f719ef4d;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index af40504..3f8175d 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,83 +1,69 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.awt.Container;
-import java.util.BitSet;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JComponent;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.utils.UrlDownloadClient;
+import javajs.util.BS;
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
-
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
{
-
- /**
- *
- */
- private AppJmol appJmolWindow;
-
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
- {
- super(sSm, pdbentry, sequenceIs, chains, protocol);
- appJmolWindow = appJmol;
- }
-
- FeatureRenderer fr = null;
-
- @Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
- : (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
- {
- if (fr == null)
- {
- fr = ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
- }
-
- return fr;
+ super(sSm, pdbentry, sequenceIs, protocol);
+ setViewer(appJmol);
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
if (console != null)
@@ -86,6 +72,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (console != null && strStatus != null)
@@ -104,7 +91,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception e)
{
- Cache.log.error("Failed to launch Jmol-associated url " + url, e);
+ Console.error("Failed to launch Jmol-associated url " + url, e);
// TODO: 2.6 : warn user if browser was not configured.
}
}
@@ -112,29 +99,26 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
@Override
public void refreshGUI()
{
+ if (getMappedStructureCount() == 0)
+ {
+ // too soon!
+ return;
+ }
// appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- appJmolWindow.updateTitleAndMenus();
- appJmolWindow.revalidate();
+ JalviewStructureDisplayI theViewer = getViewer();
+ // invokes colourbySequence() via seqColour_ActionPerformed()
+ theViewer.updateTitleAndMenus();
+ ((JComponent) theViewer).revalidate();
}
});
}
- public void updateColours(Object source)
- {
- AlignmentPanel ap = (AlignmentPanel) source, topap;
- // ignore events from panels not used to colour this view
- if (!appJmolWindow.isUsedforcolourby(ap))
- return;
- if (!isLoadingFromArchive())
- {
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
- }
- }
-
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// todo - script termination doesn't happen ?
@@ -143,90 +127,170 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
// msWalltime);
}
+ @Override
public void showUrl(String url)
{
showUrl(url, "jmol");
}
- public void newJmolPopup(boolean translateLocale, String menuName,
- boolean asPopup)
+ public void newJmolPopup(String menuName)
{
-
- jmolpopup = new JmolPopup();
- jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
+ // jmolpopup = new JmolAwtPopup();
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
- public void selectionChanged(BitSet arg0)
+ @Override
+ public void selectionChanged(BS arg0)
{
- // TODO Auto-generated method stub
-
}
- public void refreshPdbEntries()
+ @Override
+ public void showConsole(boolean b)
{
- // TODO Auto-generated method stub
+ getViewer().showConsole(b);
+ }
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow)
+ {
+ jmolViewer.setJmolCallbackListener(this);
+ // BH comment: can't do this yet [for JS only, or generally?]
+ return Platform.isJS() ? null
+ : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
- public void showConsole(boolean b)
+ @Override
+ protected void releaseUIResources()
{
- appJmolWindow.showConsole(b);
+ setViewer(null);
+ closeConsole();
}
- /**
- * add the given sequences to the mapping scope for the given pdb file handle
- *
- * @param pdbFile
- * - pdbFile identifier
- * @param seq
- * - set of sequences it can be mapped to
- */
- public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
+ @Override
+ public void releaseReferences(Object svl)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ if (svl instanceof SeqPanel)
{
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
+ getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
- Container consolePanel, String buttonsToShow)
+ public Map getJSpecViewProperty(String arg0)
{
- return new AppConsole(viewer, consolePanel, buttonsToShow);
+ // TODO Auto-generated method stub
+ return null;
}
- @Override
- protected void releaseUIResources()
+ @SuppressWarnings("unused")
+ public void cacheFiles(List files)
{
- appJmolWindow = null;
- if (console != null)
+ if (files == null)
{
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
+ return;
+ }
+ for (File f : files)
+ {
+ Platform.cacheFileData(f);
}
-
}
- @Override
- public void releaseReferences(Object svl)
+ /**
+ * Retrieves and saves as file any modelled PDB entries for which we do not
+ * already have a file saved. Returns a list of absolute paths to structure
+ * files which were either retrieved, or already stored but not modelled in
+ * the structure viewer (i.e. files to add to the viewer display).
+ *
+ * Currently only used by Jmol - similar but different code used for Chimera/X
+ * and Pymol so still need to refactor
+ *
+ * @param structureViewer
+ * UI proxy for the structure viewer
+ * @return list of absolute paths to structures retrieved that need to be
+ * added to the display
+ */
+ public List fetchPdbFiles(StructureViewerBase structureViewer)
{
- if (svl instanceof SeqPanel)
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List files = new ArrayList<>();
+ String pdbid = "";
+ try
{
- appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+ String[] filesInViewer = getStructureFiles();
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+ for (int pi = 0; pi < getPdbCount(); pi++)
+ {
+ PDBEntry strucEntry = getPdbEntry(pi);
+
+ String file = strucEntry.getFile();
+ if (file == null)
+ {
+ pdbid = strucEntry.getId();
+ try
+ {
+ file = structureViewer.fetchPdbFile(strucEntry);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("'").append(pdbid).append("'");
+ }
+ if (file != null)
+ {
+ // success
+ files.add(file);
+ }
+ else
+ {
+ errormsgs.append("'").append(pdbid).append("' ");
+ }
+ }
+ else
+ {
+ if (filesInViewer != null && filesInViewer.length > 0)
+ {
+ structureViewer.setAddingStructures(true); // already files loaded.
+ for (int c = 0; c < filesInViewer.length; c++)
+ {
+ if (Platform.pathEquals(filesInViewer[c], file))
+ {
+ file = null;
+ break;
+ }
+ }
+ }
+ if (file != null)
+ {
+ files.add(file);
+ }
+ }
+ }
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB files: " + pdbid, oomerror);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ errormsgs.append("When retrieving pdbfiles : current was: '")
+ .append(pdbid).append("'");
}
- ;
+ if (errormsgs.length() > 0)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entries_couldnt_be_retrieved", new String[]
+ { errormsgs.toString() }),
+ MessageManager.getString("label.couldnt_load_file"),
+ JvOptionPane.ERROR_MESSAGE);
+ }
+ return files;
}
+
}